Remove OBO Foundry-specific leftovers (prep for 0.1.0)#666
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ROBOT is the OBO Foundry OWL build/QC tool. The wrapper script and its ~95 MB jar were committed but never invoked anywhere in the repo. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Drops the Makefile targets that only served OBO Foundry's QC pipeline and were not reachable from 'all', 'test', or CI: - build/dashboard, clean-dashboard, reports/dashboard.html (copied a never-generated reports/robot dir and a nonexistent reports/dashboard-full.csv) - reports/robot directory target - reports/%.csv ARQ/SPARQL rule (no sparql/ directory exists) - valid-purl-report.txt and sparql-consistency-report.txt, plus the integration-test target that depended on them Also deletes util/processor.py, which backed those targets: it resolved OBO PURLs, built a purl.obolibrary.org JSON-LD context, and queried the OBO sparql.hegroup.org endpoint. The generic quality-dashboard target and the sync-* source ingests are unaffected. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
None of these are referenced anywhere in the build or tests: - auto-foundry-check.py: generated an 'OBO Foundry Criteria Checker' doc page - make-shacl-prefixes.py: emitted SHACL prefixes for purl.obolibrary.org PURLs - add_preferred_prefixes.py: added OBO preferredPrefix/resource_purl fields that are not part of the KG-Registry schema Also drops their entries from util/README.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- yaml2json.py: the generated registry/kgs.jsonld set its @context to obofoundry.github.io/registry/context.jsonld; now points at KG-Registry's own served context - check_schema.py: schema-usage report linked resources to obofoundry.org; now links to the KG-Registry resource pages - registry/README.md: replaced OBO PURL boilerplate (and a stale ../ontology/ reference) with an accurate description of the derived files - custom.js: removed a dead function that fetched the OBOFoundry obo-dash results into an empty stub Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
These exercised util/processor.py's check_urls over the OBO-specific resource_purl field. Removes the TestProcessorFTPChecking class, the test_ftp_resources.yml fixture, and their doc entries, while keeping the live retrieve-file-sizes FTP tests intact. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
A prior botched edit left a garbled code fence and a duplicated 'Getting Started'/Docker section mid-file. Restores the fence and removes the duplicate. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Summary
Release prep for 0.1.0. Removes infrastructure that was completely OBO
Foundry-specific and left over from the codebase KG-Registry was forked from,
while keeping the legitimate OBO-as-a-source feature (
sync_obo_foundry.py,the
obo-foundrycollection,org/obo-foundry/, NCIT PURL mappings, and theOBO sync tests/docs) untouched.
Net effect: ~780 fewer lines and a 95 MB binary removed, with all tests and the
Makefile build graph still intact.
Changes (one commit each)
tools/robot+ the ~95 MBtools/robot.jar; never invoked anywhere.Makefile
build/dashboard/clean-dashboard/reports/dashboard.html,reports/robot, the ARQ/SPARQLreports/%.csvrule (nosparql/dir exists),and the
valid-purl-report/sparql-consistency-report/integration-testtargets, plus
util/processor.pywhich backed them (OBO PURL resolution,purl.obolibrary.orgJSON-LD context,sparql.hegroup.orgendpoint).auto-foundry-check.py,make-shacl-prefixes.py,add_preferred_prefixes.py.generated
registry/kgs.jsonld@context, thecheck_schema.pyreport link,registry/README.md, and a dead obo-dash fetch incustom.js.processor.pyFTP tests and fixture — kept the liveretrieve-file-sizes FTP tests.
README-sitedev.md— a prior botchededit.
(Also includes the pre-existing "Bump version to 0.1.0" commit already on this branch.)
Verification
unittest discover tests).all,test,quality-dashboard,and the
sync-*ingests are unaffected.yaml2json.pyemits the corrected KG-Registry@context.Intentionally left for reviewer decision (not mechanical cleanups)
registry/context.jsonld— content is OBO-derived, but the KG visualizationfetches it live at runtime (with a fallback); rewriting it into a proper
KG-Registry context is a design task.
.github/workflows/ai-agent.yml— uses the third-partyrun-goose-oboaction with
robot-version; OBO-branded but a functional CI feature.🤖 Generated with Claude Code